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Fix CI for Zarr Python v3 #1283

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tomwhite opened this issue Jan 13, 2025 · 0 comments · Fixed by #1285
Closed

Fix CI for Zarr Python v3 #1283

tomwhite opened this issue Jan 13, 2025 · 0 comments · Fixed by #1285
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upstream Used when our build breaks due to upstream changes

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@tomwhite
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The build is failing with

FAILED sgkit/tests/io/plink/test_plink_writer.py::test_zarr_to_plink[plink_sim_10s_100v_10pmiss-\t] - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/io/plink/test_plink_writer.py::test_zarr_to_plink[example- ] - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/io/plink/test_plink_writer.py::test_zarr_to_plink[example_with_fam- ] - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/io/test_dataset.py::test_save_and_load_dataset[True] - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/io/test_dataset.py::test_save_and_load_dataset[False] - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/io/test_dataset.py::test_save_and_load_dataset__mutable_mapping - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'
FAILED sgkit/tests/test_association.py::test_regenie_loco_regression[True-numpy] - AttributeError: 'Array' object has no attribute 'compressors'
FAILED sgkit/tests/test_association.py::test_regenie_loco_regression[False-numpy] - AttributeError: 'Array' object has no attribute 'compressors'
FAILED sgkit/tests/test_regenie.py::test_regenie__glow_comparison[numpy] - AttributeError: 'Array' object has no attribute 'compressors'
FAILED sgkit/tests/test_testing.py::test_simulate_genotype_call_dataset__zarr - TypeError: Group.create_array() got an unexpected keyword argument 'overwrite'

We need to update to use the 3.0.0 release, and possibly a new release of bio2zarr.

@tomwhite tomwhite added the upstream Used when our build breaks due to upstream changes label Jan 13, 2025
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